National and Subnational estimates for Russia

Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in Russia. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively (see Methods or our paper for further explanation).

Table of Contents


Using data available up to the: 2020-07-06

Note that it takes time for infection to cause symptoms, to get tested for SARS-CoV-2 infection, for a positive test to return and ultimately to enter the case data presented here. In other words, today’s case data are only informative of new infections about two weeks ago. This is reflected in the plots below, which are by date of infection.

Expected daily confirmed cases by region


Figure 1: The results of the latest reproduction number estimates (based on estimated confirmed cases with a date of infection on the 2020-06-24) in Russia, stratified by region, can be summarised by whether confirmed cases are likely increasing or decreasing. This represents the strength of the evidence that the reproduction number in each region is greater than or less than 1, respectively (see the methods for details). Regions with fewer than 40 confirmed cases reported on a single day are not included in the analysis (light grey).

National summary

Summary (estimates as of the 2020-06-24)

Table 1: Latest estimates (as of the 2020-06-24) of the number of confirmed cases by date of infection, the expected change in daily confirmed cases, the effective reproduction number, the doubling time (when negative this corresponds to the halving time), and the adjusted R-squared of the exponential fit. The mean and 90% credible interval is shown for each numeric estimate.
Estimate
New confirmed cases by infection date 7075 (6631 – 7555)
Expected change in daily cases Unsure
Effective reproduction no. 1 (1 – 1)
Doubling/halving time (days) 360 (76 – -130)
Adjusted R-squared 0.27 (4.5e-08 – 0.64)

Confirmed cases, their estimated date of infection, and time-varying reproduction number estimates


Figure 2: A.) Confirmed cases by date of report (bars) and their estimated date of infection. B.) Time-varying estimate of the effective reproduction number. Light ribbon = 90% credible interval; dark ribbon = the 50% credible interval. Estimates from existing data are shown up to the 2020-06-24 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The vertical dashed line indicates the date of report generation.

Time-varying rate of growth and doubling time


Figure 3: A.) Time-varying estimate of the rate of growth, B.) Time-varying estimate of the doubling time in days (when negative this corresponds to the halving time), C.) The adjusted R-squared estimates indicating the goodness of fit of the exponential regression model (with values closer to 1 indicating a better fit). Estimates from existing data are shown up to the 2020-06-24. Light ribbon = 90% credible interval; dark ribbon = the 50% credible interval. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence.

Regional Breakdown

Data availability

Limitations

Summary of latest reproduction number and confirmed case count estimates by date of infection


Figure 4: Confirmed cases with date of infection on the 2020-06-24 and the time-varying estimate of the effective reproduction number (light bar = 90% credible interval; dark bar = the 50% credible interval.). Regions are ordered by the number of expected daily confirmed cases and shaded based on the expected change in daily confirmedcases. The horizontal dotted line indicates the target value of 1 for the effective reproduction no. required for control and a single case required for elimination.

Reproduction numbers over time in the six regions expected to have the most new confirmed cases


Figure 5: Time-varying estimate of the effective reproduction number (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in the regions expected to have the highest number of new confirmed cases. Estimates from existing data are shown up to the 2020-06-24 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The horizontal dotted line indicates the target value of 1 for the effective reproduction no. required for control. The vertical dashed line indicates the date of report generation.

Confirmed cases and their estimated date of infection in the six regions expected to have the most new confirmed cases


Figure 6: Confirmed cases by date of report (bars) and their estimated date of infection (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in the regions expected to have the highest number of new confirmed cases. Estimates from existing data are shown up to the 2020-06-24 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The vertical dashed line indicates the date of report generation.

Reproduction numbers over time in all regions


Figure 7: Time-varying estimate of the effective reproduction number (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in all regions. Estimates from existing data are shown up to the 2020-06-24 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The horizontal dotted line indicates the target value of 1 for the effective reproduction no. required for control. The vertical dashed line indicates the date of report generation.

Confirmed cases and their estimated date of infection in all regions

Figure 8: Confirmed cases by date of report (bars) and their estimated date of infection (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in all regions. Estimates from existing data are shown up to the 2020-06-24 from when forecasts are shown. These should be considered indicative only. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The vertical dashed line indicates the date of report generation.

Latest estimates (as of the 2020-06-24)

Table 2: Latest estimates (as of the 2020-06-24) of the number of confirmed cases by date of infection, the effective reproduction number, and the doubling time (when negative this corresponds to the halving time) in each region. The mean and 90% credible interval is shown.
Region New confirmed cases by infection date Expected change in daily cases Effective reproduction no. Doubling/halving time (days)
Adygea Republic 48 (33 – 61) Likely increasing 1.1 (0.9 – 1.3) 23 (7.8 – -24)
Altai Krai 79 (61 – 93) Unsure 1 (0.9 – 1.2) 140 (15 – -18)
Altai Republic 38 (25 – 49) Likely increasing 1.2 (0.9 – 1.4) 17 (6.3 – -25)
Amur Oblast 34 (22 – 44) Likely decreasing 0.9 (0.7 – 1.1) -21 (20 – -6.8)
Arkhangelsk Oblast 115 (96 – 133) Unsure 1 (0.9 – 1.1) -310 (21 – -19)
Astrakhan Oblast 36 (24 – 47) Unsure 1 (0.7 – 1.2) -78 (12 – -9.4)
Bashkortostan Republic 49 (35 – 61) Unsure 1 (0.8 – 1.2) -85 (15 – -11)
Belgorod Oblast 62 (45 – 74) Unsure 0.9 (0.8 – 1.1) -40 (23 – -11)
Bryansk Oblast 62 (46 – 75) Unsure 0.9 (0.8 – 1.1) -43 (22 – -11)
Buryatia Republic 38 (25 – 48) Unsure 0.9 (0.7 – 1.1) -38 (16 – -8.7)
Chechen Republic 14 (7 – 21) Unsure 1 (0.6 – 1.4) -300 (6.5 – -6.3)
Chelyabinsk Oblast 140 (116 – 158) Likely decreasing 0.9 (0.8 – 1) -24 (390 – -11)
Chuvashia Republic 59 (43 – 72) Unsure 1 (0.8 – 1.1) -110 (15 – -12)
Dagestan Republic 66 (51 – 80) Unsure 0.9 (0.8 – 1.1) -46 (22 – -11)
Ingushetia Republic 26 (16 – 35) Unsure 1 (0.7 – 1.2) -150 (9.9 – -8.5)
Irkutsk Oblast 240 (208 – 265) Likely increasing 1.1 (1 – 1.2) 44 (17 – -70)
Ivanovo Oblast 72 (55 – 86) Unsure 1 (0.8 – 1.1) -85 (19 – -13)
Kabardino-Balkarian Republic 54 (37 – 65) Likely decreasing 0.9 (0.7 – 1.1) -25 (29 – -8.9)
Kaliningrad Oblast 16 (7 – 22) Unsure 0.9 (0.6 – 1.2) -27 (10 – -5.6)
Kalmykia Republic 69 (48 – 87) Increasing 1.5 (1.2 – 1.8) 5.8 (3.9 – 12)
Kaluga Oblast 51 (36 – 63) Unsure 1 (0.8 – 1.2) 15000 (12 – -13)
Kamchatka Krai 49 (34 – 60) Unsure 1 (0.8 – 1.2) -620 (13 – -12)
Karachay-Cherkess Republic 70 (53 – 85) Unsure 0.9 (0.8 – 1.1) -41 (24 – -11)
Karelia Republic 40 (27 – 52) Unsure 1.1 (0.9 – 1.3) 29 (7.9 – -17)
Kemerovo Oblast 50 (33 – 60) Unsure 1.1 (0.9 – 1.3) 49 (9.6 – -16)
Khabarovsk Krai 84 (65 – 100) Unsure 1 (0.9 – 1.2) 70 (13 – -21)
Khakassia Republic 37 (25 – 47) Unsure 1 (0.8 – 1.3) 76 (9.6 – -12)
Khanty-Mansi Autonomous Okrug 290 (248 – 321) Unsure 1 (0.9 – 1.1) 380 (28 – -33)
Kirov Oblast 38 (23 – 48) Unsure 1 (0.7 – 1.2) -80 (13 – -9.6)
Komi Republic 65 (47 – 78) Unsure 1 (0.8 – 1.1) -390 (15 – -14)
Kostroma Oblast 24 (15 – 33) Unsure 0.9 (0.7 – 1.2) -39 (12 – -7.4)
Krasnodar Krai 61 (45 – 74) Unsure 1 (0.8 – 1.2) 84000 (14 – -14)
Krasnoyarsk Krai 140 (118 – 159) Unsure 1 (0.9 – 1.1) -110 (28 – -19)
Kurgan Oblast 31 (19 – 40) Unsure 1.1 (0.8 – 1.3) 96 (8.8 – -11)
Kursk Oblast 61 (43 – 73) Unsure 1 (0.8 – 1.1) -52 (20 – -11)
Leningrad Oblast 54 (38 – 65) Unsure 1 (0.8 – 1.2) 130 (12 – -14)
Lipetsk Oblast 40 (26 – 49) Unsure 0.9 (0.7 – 1.1) -38 (16 – -9)
Magadan Oblast 36 (21 – 46) Increasing 1.3 (1 – 1.6) 9.5 (4.7 – 5900)
Mari El Republic 30 (18 – 40) Unsure 1 (0.7 – 1.2) -54 (12 – -8.2)
Mordovia Republic 40 (27 – 50) Unsure 0.9 (0.7 – 1.1) -28 (20 – -8.3)
Moscow 736 (673 – 804) Decreasing 0.9 (0.8 – 1) -34 (-170 – -19)
Moscow Oblast 333 (287 – 366) Decreasing 0.9 (0.8 – 0.9) -19 (-49 – -12)
Murmansk Oblast 124 (102 – 142) Increasing 1.2 (1 – 1.3) 16 (8.4 – 96)
Nizhny Novgorod Oblast 234 (204 – 266) Likely increasing 1 (1 – 1.1) 51 (18 – -55)
North Ossetia - Alania Republic 25 (15 – 34) Unsure 1 (0.7 – 1.2) -60 (10 – -7.8)
Novgorod Oblast 49 (36 – 62) Unsure 1 (0.8 – 1.2) -56 (17 – -10)
Novosibirsk Oblast 104 (85 – 121) Unsure 1 (0.9 – 1.1) -470 (19 – -18)
Omsk Oblast 83 (66 – 98) Unsure 1 (0.9 – 1.2) 150 (15 – -18)
Orel Oblast 38 (27 – 50) Likely decreasing 0.9 (0.7 – 1.1) -29 (17 – -8)
Orenburg Oblast 76 (61 – 92) Unsure 1.1 (0.9 – 1.2) 37 (11 – -27)
Penza Oblast 76 (60 – 92) Unsure 1 (0.9 – 1.2) 150 (14 – -18)
Perm Krai 57 (40 – 70) Unsure 1 (0.8 – 1.1) -50 (18 – -11)
Primorsky Krai 79 (64 – 96) Unsure 1 (0.8 – 1.1) -81 (21 – -13)
Pskov Oblast 53 (38 – 66) Unsure 1 (0.8 – 1.1) -51 (17 – -10)
Rostov Oblast 98 (78 – 115) Likely decreasing 0.9 (0.8 – 1) -22 (120 – -10)
Ryazan Oblast 43 (32 – 55) Unsure 1 (0.8 – 1.2) -140 (13 – -11)
Saint Petersburg 262 (230 – 301) Likely increasing 1.1 (1 – 1.2) 30 (14 – -380)
Sakha (Yakutiya) Republic 52 (37 – 64) Likely decreasing 0.9 (0.7 – 1.1) -20 (43 – -8)
Sakhalin Oblast 31 (19 – 40) Unsure 1 (0.7 – 1.2) -130 (11 – -9.1)
Samara Oblast 68 (51 – 83) Unsure 1 (0.9 – 1.2) 54 (11 – -19)
Saratov Oblast 105 (84 – 124) Unsure 1 (0.9 – 1.1) -110 (23 – -16)
Sevastopol 6 (0 – 11) Unsure 1.3 (0.4 – 2) 37 (3 – -3.6)
Smolensk Oblast 43 (30 – 55) Unsure 1 (0.8 – 1.2) -590 (12 – -11)
Stavropol Krai 88 (70 – 104) Unsure 1 (0.9 – 1.1) -610 (18 – -17)
Sverdlovsk Oblast 250 (209 – 280) Likely increasing 1.1 (1 – 1.2) 24 (12 – 240)
Tambov Oblast 46 (34 – 60) Unsure 1 (0.8 – 1.2) -320 (13 – -12)
Tatarstan Republic 42 (30 – 54) Unsure 1 (0.8 – 1.3) 99 (10 – -13)
Tomsk Oblast 58 (43 – 70) Unsure 1 (0.8 – 1.2) -130 (16 – -13)
Tula Oblast 75 (60 – 92) Unsure 1 (0.8 – 1.1) -80 (19 – -13)
Tver Oblast 48 (33 – 60) Unsure 0.9 (0.7 – 1.1) -39 (18 – -9.4)
Tyumen Oblast 74 (57 – 89) Likely increasing 1.1 (0.9 – 1.3) 20 (8.6 – -56)
Tyva Republic 118 (98 – 136) Unsure 1 (0.8 – 1.1) -42 (37 – -14)
Udmurt Republic 23 (13 – 31) Unsure 1.1 (0.8 – 1.4) 54 (7.4 – -9.9)
Ulyanovsk Oblast 107 (90 – 126) Unsure 1 (0.9 – 1.1) -430 (20 – -18)
Vladimir Oblast 51 (36 – 63) Unsure 1 (0.8 – 1.2) -220 (14 – -12)
Volgograd Oblast 94 (75 – 111) Unsure 1 (0.8 – 1.1) -74 (23 – -15)
Vologda Oblast 23 (14 – 32) Unsure 1.1 (0.8 – 1.4) 55 (7 – -9.5)
Voronezh Oblast 168 (146 – 190) Likely decreasing 0.9 (0.9 – 1) -44 (60 – -16)
Yamalo-Nenets Autonomous Okrug 194 (168 – 217) Increasing 1.1 (1 – 1.2) 26 (13 – -370)
Yaroslavl Oblast 45 (31 – 56) Unsure 1 (0.8 – 1.2) -810 (12 – -12)
Zabaykalsky Krai 58 (42 – 71) Unsure 1 (0.8 – 1.1) -59 (18 – -11)

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Mironov, Sergey. 2020. “COVID-19 Data from Jhu Csse, Updated with Details on Russian Regions.” Github Repository. https://github.com/grwlf/COVID-19_plus_Russia.

Xu, Bo, Bernardo Gutierrez, Sarah Hill, Samuel Scarpino, Alyssa Loskill, Jessie Wu, Kara Sewalk, et al. n.d. “Epidemiological Data from the nCoV-2019 Outbreak: Early Descriptions from Publicly Available Data.” http://virological.org/t/epidemiological-data-from-the-ncov-2019-outbreak-early-descriptions-from-publicly-available-data/337.